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Sloane mentions taking a bullet for Jack in "Breaking Point."
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Lauren dropped a piece of note into a garbage can is very much like how Sydney and the real CIA communicate during the first season. Of course, Vaughn took the note out of the trash and found that it was simply a to-do list.
Only one item on the list was checked, and it was to "pay the bills". Vaughn being the intelligent officer that he is should have kept the list for himself - in case it was some coded message for someone from the Covenant to obtain. He should know.
Besides, why would Lauren discard a list that still had items unchecked? Logically, she still needs to do them, cause almost all were unchecked.
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Flash drives (such as the USB memory stick that the data was on) are not venerable to magnetic fields, and an EMP strong enough to wipe the drive would also have fried the computer in a very obvious way. A strong enough XRay bean could mess up the data, but probably also given the wearer of the ring cancer in short order. The explanation of solar flare activity is just nonsense (unless of course you were in a high earth orbit).
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Goof:
When Vaughn discovers the safe room door in Dr. Viadro's house, the keypad LEDs show it to be unlocked (one green LED). But when he approaches the keypad to to attempt a circumvent of the electronics, the LEDs indicate it is in a locked state again (two red LEDs).
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Goof: When Marshall gives Sydney and Vaughn the sun glasses he presses the button on the left side. When Sydney sends the hacker a message she presses on the right side.
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Why did Lauren tell Vaughn she got a call from her mother blaming her for what happened to her father? That obviously didn't happen, and unless she knew that Vaughn was hearing her conversation with Sark, her excuse is a little too convenient to cover that up.
She probably figured that she had been spotted wandering around the mall suspiciously while on her cellphone and came up with an excuse that would cover her actions. She got lucky in coming up with an excuse which also explained the outraged tone Vaughn heard her use.
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Goof:
Initially in the Operations Center, and during the virus briefing, Sydney has no bangs. Then she and Vaughn go into Marshall's office and she has bangs. Apparently she stopped off at the bathroom with a curler to get them just right in the space of a minute or two.
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Goof: When Dixon visited Sloane earlier, Sloane was chained up for security. But when Jack visits him, Sloane is unchained.
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When Dr. Viadro shoves the coat aside to reveal the code panel, the actor inadvertently knocks the loosely-fastened prop loose, then shoves it back into place before entering the code.
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Dixon specifically says that the notes from Dr. Barnett's sessions with Sloane reveal that Sloane was sleeping with Irina. But...the only time Sloane and Barnett discussed that was when they were on a date, not in a session.
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Does Barnett as a psychologist have patient-doctor confidentiality? She promised Sloane she did. And she's had Sydney and Jack tell her deep dark secrets by promising it. But here, Dixon just goes through her notes and finds out everything about her sessions with Sloane. No wonder Jack doesn't want to talk to her.